Marius,
 
Hmm...are you perhaps looking at the output before the file is closed and/or flushed? You should issue ndx.flush() or ndx.close() before attempting to use the output file.
 
Cheres,
Warren
 

From: pymol-users-bounces@lists.sourceforge.net [mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf Of Marius Retegan
Sent: Friday, June 27, 2008 9:01 AM
To: pymol-users
Subject: Re: [PyMOL] writing selection to a external file

Hi,
It seems that I run into a little problem. When I try to write a large selection I get only a partial list of ID. If for example I print ID after the iterate command, all the list is printed into pymol window. Do you have any idea why?
I run Pymol 1.1pre5 under Fedora 8.


On Fri, Jun 27, 2008 at 1:36 PM, Tsjerk Wassenaar <tsjerkw@gmail.com> wrote:
Hi,

This should've gone to the list... (isn't there an option "send
replies to list rather than to poster" to the mailing list?)

Tsjerk

On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar <tsjerkw@gmail.com> wrote:
> Hi Marius,
>
> You want iterate.
> You do have to make sure though that the numbering of your atoms in
> the structure file is correct. Than you can do:
>
> ndx=open("index.ndx","w")
> ndx.write("[ MyIndex ]\n")
> iterate selection, ndx.write("%d\n" % ID)
> ndx.close()
>
> I did make the assumption that you wanted the atom id's rather than
> the residue id's, since the latter are of no use to Gromacs.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan
> <marius.s.retegan@gmail.com> wrote:
>> Hi All,
>> I'm using pymol to select (by residue) all the atoms around 10 angstroms
>> from a certain atom. Now I would like to write the residue id's of my
>> selection to an external file, so that I can integrated in the ndx file from
>> Gromacs. Do you have any idea how I could do that?
>>
>> Thanks,
>>
>> Marius Retegan
>>
>> -------------------------------------------------------------------------
>> Check out the new SourceForge.net Marketplace.
>> It's the best place to buy or sell services for
>> just about anything Open Source.
>> http://sourceforge.net/services/buy/index.php
>> _______________________________________________
>> PyMOL-users mailing list
>> PyMOL-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>



--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

-------------------------------------------------------------------------
Check out the new SourceForge.net Marketplace.
It's the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php
_______________________________________________
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users